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Sodium in PDB 3kzw: Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col

Enzymatic activity of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col

All present enzymatic activity of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col:
3.4.11.1;

Protein crystallography data

The structure of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col, PDB code: 3kzw was solved by J.Hattne, I.Dubrovska, A.Halavaty, G.Minasov, P.Scott, L.Shuvalova, J.Winsor, Z.Otwinowski, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.62 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 143.383, 154.733, 340.101, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24

Other elements in 3kzw:

The structure of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col also contains other interesting chemical elements:

Chlorine (Cl) 67 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col (pdb code 3kzw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col, PDB code: 3kzw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in 3kzw

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Sodium binding site 1 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na497

b:29.4
occ:1.00
 O A:HOH537 2.3 2.0 1.0
O A:HOH599 2.4 9.1 1.0
O A:THR446 2.5 2.8 1.0
O A:GLY450 2.5 2.8 1.0
OG A:SER387 3.0 2.8 1.0
OG A:SER449 3.3 2.7 1.0
O A:HOH514 3.4 2.0 1.0
C A:THR446 3.6 2.7 1.0
C A:GLY450 3.7 2.7 1.0
N A:GLY450 4.0 2.7 1.0
OD1 A:ASN388 4.2 2.9 1.0
CB A:SER387 4.2 2.6 1.0
CA A:GLY450 4.3 2.6 1.0
N A:HIS447 4.4 2.7 1.0
CA A:HIS447 4.4 2.6 1.0
CB A:THR446 4.4 2.7 1.0
O A:HIS447 4.5 2.7 1.0
CA A:THR446 4.5 2.7 1.0
CB A:SER449 4.5 2.6 1.0
C A:SER449 4.5 2.7 1.0
C A:HIS447 4.6 2.6 1.0
N A:GLN451 4.7 2.7 1.0
N A:SER449 4.7 2.6 1.0
CA A:SER449 4.9 2.7 1.0
OG1 A:THR446 4.9 2.8 1.0
O A:THR452 4.9 2.7 1.0
CA A:GLN451 5.0 2.7 1.0

Sodium binding site 2 out of 19 in 3kzw

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Sodium binding site 2 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na498

b:21.6
occ:1.00
 O A:HOH552 2.4 2.0 1.0
OG1 A:THR464 2.7 2.7 1.0
O A:GLY461 2.8 2.8 1.0
OD1 A:ASP379 3.3 3.2 1.0
OD2 A:ASP379 3.3 3.1 1.0
O A:THR464 3.3 2.7 1.0
CG A:ASP379 3.7 3.0 1.0
O A:ALA460 3.7 2.8 1.0
C A:GLY461 3.7 2.7 1.0
CB A:THR464 4.0 2.6 1.0
CA A:GLY461 4.0 2.7 1.0
C A:THR464 4.0 2.6 1.0
CA A:THR464 4.3 2.6 1.0
N A:THR464 4.4 2.6 1.0
C A:ALA460 4.6 2.7 1.0
N A:GLY461 4.8 2.7 1.0
O A:ASP379 4.9 2.8 1.0
N A:THR465 5.0 2.6 1.0
N A:PRO462 5.0 2.6 1.0

Sodium binding site 3 out of 19 in 3kzw

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Sodium binding site 3 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na498

b:40.7
occ:1.00
 O B:HOH540 2.3 2.0 1.0
O B:ALA460 2.9 2.8 1.0
OG1 B:THR464 3.2 2.7 1.0
OD1 B:ASP379 3.4 3.2 1.0
O B:GLY461 3.4 2.8 1.0
O B:HOH520 3.4 2.0 1.0
CA B:GLY461 3.9 2.7 1.0
C B:ALA460 4.0 2.7 1.0
C B:GLY461 4.1 2.7 1.0
CG B:ASP379 4.2 3.1 1.0
OD2 B:ASP379 4.2 3.2 1.0
CD1 B:ILE374 4.3 2.6 1.0
N B:GLY461 4.4 2.7 1.0
O B:THR464 4.6 2.7 1.0
CB B:THR464 4.6 2.6 1.0

Sodium binding site 4 out of 19 in 3kzw

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Sodium binding site 4 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na498

b:23.3
occ:1.00
 O C:HOH546 2.2 6.8 1.0
O C:HOH550 2.2 2.0 1.0
O C:THR446 2.5 2.8 1.0
O C:GLY450 2.6 2.8 1.0
OG C:SER449 2.7 2.6 1.0
OG C:SER387 2.9 2.8 1.0
C C:GLY450 3.6 2.7 1.0
C C:THR446 3.7 2.7 1.0
N C:GLY450 3.9 2.6 1.0
CB C:SER387 3.9 2.6 1.0
CB C:SER449 4.0 2.6 1.0
OD1 C:ASN388 4.0 2.8 1.0
O C:THR452 4.2 2.7 1.0
C C:SER449 4.2 2.7 1.0
O C:HOH526 4.3 2.0 1.0
CA C:GLY450 4.3 2.7 1.0
CB C:THR446 4.3 2.6 1.0
CA C:THR446 4.5 2.7 1.0
CA C:SER449 4.5 2.7 1.0
N C:SER449 4.6 2.6 1.0
CB C:HIS454 4.6 2.6 1.0
N C:GLN451 4.6 2.7 1.0
N C:HIS447 4.7 2.7 1.0
O C:SER387 4.7 2.8 1.0
CA C:HIS447 4.8 2.6 1.0
CA C:GLN451 4.8 2.7 1.0
O C:SER449 4.9 2.7 1.0
O C:HIS447 4.9 2.8 1.0
C C:HIS447 4.9 2.7 1.0
ND1 C:HIS454 5.0 2.7 1.0

Sodium binding site 5 out of 19 in 3kzw

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Sodium binding site 5 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na498

b:21.7
occ:1.00
 O D:HOH572 2.4 2.0 1.0
O D:THR446 2.4 2.8 1.0
O D:GLY450 2.5 2.8 1.0
OG D:SER449 2.8 2.7 1.0
OG D:SER387 3.0 2.8 1.0
C D:GLY450 3.6 2.7 1.0
C D:THR446 3.6 2.7 1.0
N D:GLY450 3.9 2.7 1.0
CB D:SER387 4.1 2.6 1.0
CB D:SER449 4.1 2.6 1.0
OD1 D:ASN388 4.1 2.8 1.0
CA D:GLY450 4.2 2.6 1.0
C D:SER449 4.3 2.7 1.0
CB D:THR446 4.4 2.7 1.0
O D:THR452 4.5 2.7 1.0
CA D:THR446 4.5 2.7 1.0
N D:HIS447 4.5 2.7 1.0
CA D:SER449 4.5 2.7 1.0
N D:SER449 4.5 2.6 1.0
N D:GLN451 4.6 2.7 1.0
CA D:HIS447 4.6 2.6 1.0
O D:HIS447 4.6 2.8 1.0
C D:HIS447 4.7 2.6 1.0
CA D:GLN451 4.9 2.7 1.0
CB D:HIS454 4.9 2.6 1.0
O D:SER449 4.9 2.7 1.0
O D:SER387 4.9 2.8 1.0

Sodium binding site 6 out of 19 in 3kzw

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Sodium binding site 6 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na499

b:18.9
occ:1.00
 O D:GLY461 2.7 2.8 1.0
OG1 D:THR464 2.8 2.7 1.0
OD2 D:ASP379 3.1 3.2 1.0
O D:THR464 3.2 2.7 1.0
OD1 D:ASP379 3.2 3.2 1.0
CG D:ASP379 3.5 3.1 1.0
C D:GLY461 3.7 2.7 1.0
C D:THR464 3.9 2.6 1.0
O D:ALA460 3.9 2.8 1.0
CB D:THR464 4.0 2.7 1.0
CA D:GLY461 4.0 2.7 1.0
CA D:THR464 4.3 2.6 1.0
N D:THR464 4.3 2.6 1.0
O D:HOH548 4.4 2.0 1.0
O D:ASP379 4.8 2.8 1.0
C D:ALA460 4.8 2.7 1.0
N D:THR465 4.8 2.6 1.0
N D:GLY461 4.9 2.7 1.0
N D:PRO462 4.9 2.6 1.0
CB D:ASP379 5.0 2.8 1.0

Sodium binding site 7 out of 19 in 3kzw

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Sodium binding site 7 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na498

b:30.3
occ:1.00
 O E:HOH547 2.6 2.0 1.0
O E:GLY450 2.7 2.8 1.0
OG E:SER449 2.7 2.7 1.0
OG E:SER387 2.8 2.8 1.0
O E:THR452 3.1 2.7 1.0
OD1 E:ASN388 3.4 2.9 1.0
O E:THR446 3.5 2.8 1.0
C E:GLY450 3.7 2.7 1.0
O E:SER387 3.7 2.9 1.0
CB E:SER387 3.7 2.6 1.0
CB E:SER449 4.0 2.7 1.0
CB E:HIS454 4.0 2.6 1.0
C E:THR452 4.2 2.7 1.0
C E:GLN451 4.2 2.7 1.0
C E:SER387 4.2 2.7 1.0
N E:THR452 4.3 2.6 1.0
CA E:GLN451 4.3 2.7 1.0
N E:GLY450 4.3 2.7 1.0
C E:SER449 4.4 2.7 1.0
N E:GLN451 4.4 2.7 1.0
CG E:ASN388 4.4 2.7 1.0
CA E:SER387 4.6 2.7 1.0
CA E:GLY450 4.7 2.6 1.0
CB E:ASN388 4.7 2.6 1.0
C E:THR446 4.7 2.7 1.0
O E:SER449 4.7 2.7 1.0
O E:GLN451 4.7 2.8 1.0
CA E:SER449 4.7 2.7 1.0
N E:HIS454 4.7 2.6 1.0
CA E:THR452 4.8 2.6 1.0
ND1 E:HIS454 4.9 2.7 1.0
CB E:THR446 4.9 2.7 1.0
CG E:HIS454 4.9 2.6 1.0

Sodium binding site 8 out of 19 in 3kzw

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Sodium binding site 8 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na499

b:38.3
occ:1.00
 O E:GLY461 2.6 2.8 1.0
OG1 E:THR464 2.7 2.7 1.0
OD2 E:ASP379 3.0 3.2 1.0
O E:THR464 3.0 2.7 1.0
OD1 E:ASP379 3.2 3.2 1.0
CG E:ASP379 3.5 3.1 1.0
C E:GLY461 3.6 2.7 1.0
C E:THR464 3.7 2.6 1.0
CB E:THR464 3.9 2.7 1.0
O E:ALA460 3.9 2.8 1.0
CA E:GLY461 4.0 2.7 1.0
CA E:THR464 4.2 2.7 1.0
N E:THR464 4.2 2.6 1.0
O E:ASP379 4.7 2.8 1.0
N E:THR465 4.7 2.6 1.0
C E:ALA460 4.8 2.7 1.0
N E:PRO462 4.9 2.6 1.0
N E:GLY461 4.9 2.6 1.0
CB E:ASP379 5.0 2.8 1.0

Sodium binding site 9 out of 19 in 3kzw

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Sodium binding site 9 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na497

b:38.0
occ:1.00
 O F:GLY461 2.6 2.8 1.0
OG1 F:THR464 2.7 2.7 1.0
O F:THR464 3.1 2.7 1.0
OD2 F:ASP379 3.1 3.1 1.0
OD1 F:ASP379 3.2 3.2 1.0
CG F:ASP379 3.5 3.0 1.0
C F:GLY461 3.6 2.7 1.0
C F:THR464 3.8 2.7 1.0
O F:ALA460 3.9 2.8 1.0
CB F:THR464 3.9 2.7 1.0
O F:HOH503 3.9 2.6 1.0
CA F:GLY461 4.0 2.7 1.0
CA F:THR464 4.2 2.7 1.0
N F:THR464 4.2 2.6 1.0
O F:ASP379 4.7 2.8 1.0
N F:THR465 4.7 2.6 1.0
C F:ALA460 4.8 2.7 1.0
N F:PRO462 4.9 2.6 1.0
N F:GLY461 4.9 2.7 1.0

Sodium binding site 10 out of 19 in 3kzw

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Sodium binding site 10 out of 19 in the Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Cytosol Aminopeptidase From Staphylococcus Aureus Col within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na497

b:43.1
occ:1.00
 O G:GLY450 2.6 2.8 1.0
OG G:SER449 2.6 2.7 1.0
O G:THR446 2.8 2.8 1.0
OG G:SER387 2.8 2.7 1.0
C G:GLY450 3.6 2.7 1.0
CB G:SER387 3.8 2.6 1.0
OD1 G:ASN388 3.8 2.9 1.0
O G:THR452 3.9 2.7 1.0
C G:THR446 3.9 2.7 1.0
CB G:SER449 3.9 2.7 1.0
N G:GLY450 4.0 2.7 1.0
C G:SER449 4.3 2.7 1.0
O G:SER387 4.4 2.8 1.0
CB G:HIS454 4.4 2.6 1.0
CA G:GLY450 4.4 2.6 1.0
CB G:THR446 4.5 2.7 1.0
CA G:SER449 4.5 2.7 1.0
N G:GLN451 4.5 2.7 1.0
O G:HOH521 4.6 2.0 1.0
CA G:THR446 4.6 2.7 1.0
CA G:GLN451 4.7 2.7 1.0
N G:SER449 4.7 2.7 1.0
C G:SER387 4.8 2.7 1.0
O G:SER449 4.8 2.7 1.0
C G:GLN451 4.8 2.7 1.0
N G:THR452 4.9 2.6 1.0
ND1 G:HIS454 4.9 2.7 1.0
CA G:SER387 4.9 2.7 1.0
N G:HIS447 4.9 2.6 1.0
CG G:ASN388 4.9 2.8 1.0
C G:THR452 5.0 2.6 1.0

Reference:

J.Hattne, I.Dubrovska, A.Halavaty, G.Minasov, P.Scott, L.Shuvalova, J.Winsor, Z.Otwinowski, Center For Structural Genomics Of Infectiousdiseases (Csgid). N/A N/A.
Page generated: Mon Oct 7 11:16:25 2024

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